API for bambu
Reference-guided isoform reconstruction and quantification for long read RNA-Seq data
| Global functions | |
|---|---|
| .onUnload | Source code |
| abundance_quantification | Source code |
| addGeneIdsToReadClassTable | Source code |
| assignGeneIDbyMaxMatch | Source code |
| assignGeneIDexonMatch | Source code |
| assignNewGeneIds | Source code |
| bambu | Man page Source code |
| bambu.constructReadClass | Source code |
| bambu.extendAnnotations | Source code |
| bambu.quantDT | Source code |
| bambu.quantify | Source code |
| calculateDistToAnnotation | Source code |
| calculateFirstLastExonsDist | Source code |
| calculateStrandedReadCounts | Source code |
| checkInputs | Source code |
| checkStartSequence | Source code |
| constructSplicedReadClassTables | Source code |
| constructUnsplicedReadClasses | Source code |
| correctJunctionFromPrediction | Source code |
| correctReadTableStrand | Source code |
| createExonByReadClass | Source code |
| createExonsByReadClass | Source code |
| createIntronTmp | Source code |
| createJunctionTable | Source code |
| createModelforJunctionReads | Source code |
| createReadMatrix | Source code |
| createReadTable | Source code |
| createRefFromReadClassSE | Source code |
| createSEforSplicedTx | Source code |
| createSEforUnsplicedTx | Source code |
| createSpliceMetadata | Source code |
| cutStartEndFromGrangesList | Source code |
| dropGrangesListElementsByWidth | Source code |
| emWithL1 | Source code |
| em_theta | Source code |
| evalAnnotationOverlap | Source code |
| evalutePerformance | Source code |
| exonsintronsByReadClass | Source code |
| extdannotateSplicedReads | Source code |
| extdannotateUnsplicedReads | Source code |
| extendGrangesListElements | Source code |
| filterTranscripts | Source code |
| findHighConfidenceJunctions | Source code |
| findJunctionsByStrand | Source code |
| findSpliceOverlapsByDist | Source code |
| findSpliceOverlapsQuick | Source code |
| findUniqueJunctions | Source code |
| fitBinomialModel | Source code |
| genFilteredAnTable | Source code |
| generateExonsByReadClass | Source code |
| getEmptyClassFromSE | Source code |
| getMinimumEqClassByTx | Source code |
| helpFun | Source code |
| includeOverlapReadClass | Source code |
| initiateHitsDF | Source code |
| isore.combineTranscriptCandidates | Source code |
| isore.constructReadClasses | Source code |
| isore.estimateDistanceToAnnotations | Source code |
| isore.extendAnnotations | Source code |
| junctionStrandCorrection | Source code |
| myCompatibleTranscription | Source code |
| myGaps | Source code |
| myOneMatch | Source code |
| plotAnnotation | Source code |
| plotAnnotation_withExpression | Source code |
| plotBambu | Man page Source code |
| plotHeatmap | Source code |
| plotPCA | Source code |
| predictSpliceJunctions | Source code |
| prepSEforUnsplicedTx | Source code |
| prepareAnnotations | Man page Source code |
| prepareAnnotationsFromGTF | Source code |
| prepareDataFromBam | Source code |
| processReads | Source code |
| rangesDist | Source code |
| readFromGTF | Man page Source code |
| removeTranscriptsWIdenJunct | Source code |
| run_parallel | Source code |
| selectEndExonsFromGrangesList | Source code |
| selectStartExonsFromGrangesList | Source code |
| setBiocParallelParameters | Source code |
| setEmParameters | Source code |
| setIsoreParameters | Source code |
| spliceStrand | Source code |
| testSpliceSites | Source code |
| transcriptToGeneExpression | Man page Source code |
| unlistIntrons | Source code |
| updateJunctionwimprove | Source code |
| updateParameters | Source code |
| updateStrandScoreByRead | Source code |
| updateWIntronMatches | Source code |
| useRefJunctionForConflict | Source code |
| writeBambuOutput | Man page Source code |
| writeToGTF | Man page Source code |
